Questions
========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=4 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=4 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Allowing multi-threading with up to 4 threads.
preparing gene to GO mapping data... preparing IC data... preparing gene to GO mapping data... preparing IC data... preparing gene to GO mapping data... preparing IC data...
| Wald padj < 0.05 | LFC > 0 (Wald padj < 0.05) | LFC < 0 (Wald padj < 0.05) | |
|---|---|---|---|
| GF VS SPF (F, 8w) | 392 | 192 | 200 |
| GF VS SPF (M, 8w) | 161 | 76 | 85 |
| GF VS SPF (F, 52w) | 738 | 316 | 422 |
| GF VS SPF (M, 52w) | 393 | 145 | 248 |
| GF VS SPF (F, 104w) | 2038 | 846 | 1192 |
| GF VS SPF (M, 104w) | 2172 | 898 | 1274 |
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”
Differentially expressed genes
| Age | F | M |
|---|---|---|
| 8w | GF vs SPF | GF vs SPF |
| 52w | GF vs SPF | GF vs SPF |
| 104w | GF vs SPF | GF vs SPF |
Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)
Network based on description similarity
| F | M | |
|---|---|---|
| 8w | GF vs SPF | GF vs SPF |
| 52w | GF vs SPF | GF vs SPF |
| 104w | GF vs SPF | GF vs SPF |
GF VS SPF (F, 8w)
GF VS SPF (M, 8w)
GF VS SPF (F, 52w)
GF VS SPF (M, 52w)
GF VS SPF (F, 104w)
GF VS SPF (M, 104w)
Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)
Warning message: “Removed 7 rows containing missing values (geom_point).”
Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)
Warning message: “Removed 7 rows containing missing values (geom_point).”
[1] "Note: 11 of 4057 unique input IDs unmapped." [1] "Note: 11 of 4057 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)'
Pathway graphs available at ../results/dge/type-effect/type_gender_age/over_repr_kegg/
[1] "Note: 11 of 4057 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”
[1] "Note: 11 of 4057 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)'
Pathway graphs available at ../results/dge/type-effect/type_gender_age/under_repr_kegg/
Protocol: 2 months old female mices (GF vs SPF)